1
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Gaines MC, Sivabalasarma S, Isupov MN, Haque RU, McLaren M, Hanus C, Gold VAM, Albers SV, Daum B. CryoEM reveals the structure of an archaeal pilus involved in twitching motility. Nat Commun 2024; 15:5050. [PMID: 38877033 PMCID: PMC11178815 DOI: 10.1038/s41467-024-45831-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/02/2024] [Indexed: 06/16/2024] Open
Abstract
Amongst the major types of archaeal filaments, several have been shown to closely resemble bacterial homologues of the Type IV pili (T4P). Within Sulfolobales, member species encode for three types of T4P, namely the archaellum, the UV-inducible pilus system (Ups) and the archaeal adhesive pilus (Aap). Whereas the archaellum functions primarily in swimming motility, and the Ups in UV-induced cell aggregation and DNA-exchange, the Aap plays an important role in adhesion and twitching motility. Here, we present a cryoEM structure of the Aap of the archaeal model organism Sulfolobus acidocaldarius. We identify the component subunit as AapB and find that while its structure follows the canonical T4P blueprint, it adopts three distinct conformations within the pilus. The tri-conformer Aap structure that we describe challenges our current understanding of pilus structure and sheds new light on the principles of twitching motility.
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Affiliation(s)
- Matthew C Gaines
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK
| | - Shamphavi Sivabalasarma
- Institute of Biology, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Risat Ul Haque
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266 - Université Paris Cité, Paris, France
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK
| | - Sonja-Verena Albers
- Institute of Biology, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBBS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, UK.
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK.
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2
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Gambelli L, McLaren M, Conners R, Sanders K, Gaines MC, Clark L, Gold VAM, Kattnig D, Sikora M, Hanus C, Isupov MN, Daum B. Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius. eLife 2024; 13:e84617. [PMID: 38251732 PMCID: PMC10903991 DOI: 10.7554/elife.84617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/19/2024] [Indexed: 01/23/2024] Open
Abstract
Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single-particle cryo electron microscopy, cryo electron tomography, and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes in SlaA play important roles in S-layer assembly.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Matthew C Gaines
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Lewis Clark
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniel Kattnig
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, Frankfurt, Germany
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266 - Université Paris Cité, Paris, France
- GHU Psychiatrie et Neurosciences de Paris, Paris, France
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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3
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Vershinin Z, Zaretsky M, Guan Z, Eichler J. Agl28 and Agl29 are key components of a Halobacterium salinarum N-glycosylation pathway. FEMS Microbiol Lett 2023; 370:fnad017. [PMID: 36866517 PMCID: PMC10022576 DOI: 10.1093/femsle/fnad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/04/2023] Open
Abstract
Although Halobacterim salinarum provided the first example of N-glycosylation outside the Eukarya, only recently has attention focused on delineating the pathway responsible for the assembly of the N-linked tetrasaccharide decorating selected proteins in this haloarchaeon. In the present report, the roles of VNG1053G and VNG1054G, two proteins encoded by genes clustered together with a set of genes demonstrated to encode N-glycosylation pathway components, were considered. Relying on both bioinformatics and gene deletion and subsequent mass spectrometry analysis of known N-glycosylated proteins, VNG1053G was determined to be the glycosyltransferase responsible for addition of the linking glucose, while VNG1054G was deemed to be the flippase that translocates the lipid-bound tetrasaccharide across the plasma membrane to face the cell exterior, or to contribute to such activity. As observed with Hbt. salinarum lacking other components of the N-glycosylation machinery, both cell growth and motility were compromised in the absence of VNG1053G or VNG1054G. Thus, given their demonstrated roles in Hbt. salinarum N-glycosylation, VNG1053G and VNG1054G were re-annotated as Agl28 and Agl29, according to the nomenclature used to define archaeal N-glycosylation pathway components.
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Affiliation(s)
- Zlata Vershinin
- Department of Life Sciences, Ben-Gurion University of the Negev, PO Box 653, Beersheva 84105, Israel
| | - Marianna Zaretsky
- Department of Life Sciences, Ben-Gurion University of the Negev, PO Box 653, Beersheva 84105, Israel
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, United States
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, PO Box 653, Beersheva 84105, Israel
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4
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Notaro A, Vershinin Z, Guan Z, Eichler J, De Castro C. An N-linked tetrasaccharide from Halobacterium salinarum presents a novel modification, sulfation of iduronic acid at the O-3 position. Carbohydr Res 2022; 521:108651. [PMID: 36037649 DOI: 10.1016/j.carres.2022.108651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Halobacterium salinarum, a halophilic archaeon that grows at near-saturating salt concentrations, provided the first example of N-glycosylation outside Eukarya. Yet, almost 50 years later, numerous aspects of such post-translational protein processing in this microorganism remain to be determined, including the architecture of glycoprotein-bound glycans. In the present report, nuclear magnetic resonance spectroscopy was used to define a tetrasaccharide N-linked to both archaellins, building blocks of the archaeal swimming device (the archaellum), and the S-layer glycoprotein that comprises the protein shell surrounding the Hbt. salinarum cell as β-GlcA(2S)-(1 → 4)-α-IdoA(3S)-(1 → 4)-β-GlcA-(1 → 4)-β-Glc-Asn. The structure of this tetrasaccharide fills gaps remaining from previous studies, including confirmation of the first known inclusion of iduronic acid in an archaeal N-linked glycan. At the same time, the sulfation of this iduronic acid at the O-3 position has not, to the best of our knowledge, been previously seen. As such, this may represent yet another unique facet of N-glycosylation in Archaea.
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Affiliation(s)
- Anna Notaro
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, Italy
| | - Zlata Vershinin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel.
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, Italy.
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5
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Amin K, Tranchimand S, Benvegnu T, Abdel-Razzak Z, Chamieh H. Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology. Biomolecules 2021; 11:1557. [PMID: 34827555 PMCID: PMC8615776 DOI: 10.3390/biom11111557] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/09/2021] [Accepted: 10/16/2021] [Indexed: 01/18/2023] Open
Abstract
Hyperthermophilic Archaea colonizing unnatural habitats of extremes conditions such as volcanoes and deep-sea hydrothermal vents represent an unmeasurable bioresource for enzymes used in various industrial applications. Their enzymes show distinct structural and functional properties and are resistant to extreme conditions of temperature and pressure where their mesophilic homologs fail. In this review, we will outline carbohydrate-active enzymes (CAZymes) from hyperthermophilic Archaea with specific focus on the two largest families, glycoside hydrolases (GHs) and glycosyltransferases (GTs). We will present the latest advances on these enzymes particularly in the light of novel accumulating data from genomics and metagenomics sequencing technologies. We will discuss the contribution of these enzymes from hyperthermophilic Archaea to industrial applications and put the emphasis on newly identifed enzymes. We will highlight their common biochemical and distinct features. Finally, we will overview the areas that remain to be explored to identify novel promising hyperthermozymes.
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Affiliation(s)
- Khadija Amin
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Sylvain Tranchimand
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Thierry Benvegnu
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Ziad Abdel-Razzak
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Faculty of Sciences, Lebanese University, Rafic Hariri Campus, Beirut P.O. Box 6573, Lebanon
| | - Hala Chamieh
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Faculty of Sciences, Lebanese University, Rafic Hariri Campus, Beirut P.O. Box 6573, Lebanon
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6
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Vershinin Z, Zaretsky M, Guan Z, Eichler J. Revisiting N-glycosylation in Halobacterium salinarum: Characterizing a dolichol phosphate- and glycoprotein-bound tetrasaccharide. Glycobiology 2021; 31:1645-1654. [PMID: 34314490 DOI: 10.1093/glycob/cwab080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/15/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022] Open
Abstract
Although Halobacterium salinarum provided the first example of N-glycosylation outside the Eukarya, much regarding such post-translational modification in this halophilic Archaea remains either unclear or unknown. The composition of an N-linked glycan decorating both the S-layer glycoprotein and archaellins offers one such example. Originally described some 40 years ago, reports from that time on have presented conflicted findings regarding the composition of this glycan, as well as differences between the protein-bound glycan and that version of the glycan attached to the lipid upon which it is assembled. To clarify these points, liquid chromatography-electrospray ionization mass spectrometry was employed here to revisit the composition of this glycan both when attached to selected asparagine residues of target proteins and when bound to the lipid dolichol phosphate upon which the glycan is assembled. Such efforts revealed the N-linked glycan as corresponding to a tetrasacchride comprising a hexose, a sulfated hexuronic acid, a hexuronic acid and a second sulfated hexuronic acid. When attached to dolichol phosphate but not to proteins, the same tetrasaccharide is methylated on the final sugar. Moreover, in the absence of the oligosaccharyltransferase AglB, there is an accumulation of the dolichol phosphate-linked methylated and disulfated tetrasacchride. Knowing the composition of this glycan at both the lipid- and protein-bound stages, together with the availability of gene deletion approaches for manipulating Halobacterium salinarum, will allow delineation of the N-glycosylation pathway in this organism.
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Affiliation(s)
- Zlata Vershinin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Marianna Zaretsky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham NC, USA
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
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7
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Chiang CY, Chou CC, Chang HY, Hsu MF, Pao PJ, Chiang MH, Wang AHJ. Biochemical and molecular dynamics studies of archaeal polyisoprenyl pyrophosphate phosphatase from Saccharolobus solfataricus. Enzyme Microb Technol 2020; 139:109585. [DOI: 10.1016/j.enzmictec.2020.109585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/29/2022]
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8
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Evolutionary considerations of the oligosaccharyltransferase AglB and other aspects of N-glycosylation across Archaea. Mol Phylogenet Evol 2020; 153:106951. [PMID: 32889138 DOI: 10.1016/j.ympev.2020.106951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 08/01/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022]
Abstract
Various biological markers in members of the TACK and Asgard archaeal super-phyla show Eukarya-like traits. These include the oligosaccharyltransferase, responsible for transferring glycans from the lipid carrier upon which they are assembled onto selected asparagine residues of target proteins during N-glycosylation. In Archaea, oligosaccharyltransferase activity is catalyzed by AglB. To gain deeper insight into AglB and N-glycosylation across archaeal phylogeny, bioinformatics approaches were employed to address variability in AglB sequence motifs involved in enzyme activity, construct a phylogenetic tree based on AglB sequences, search for archaeal homologues of non-catalytic subunits of the multimeric eukaryal oligosaccharyltransferase complex and predict the presence of aglB-based clusters of glycosylation-related genes in the Euryarchaeota and the DPANN, TACK and Asgard super-phyla. In addition, site-directed mutagenesis and mass spectrometry were employed to study the natural variability in the WWDXG motif central to oligosaccharyltransferase activity seen in archaeal AglB. The results clearly distinguish AglB from members of the DPANN super-phylum and the Euryarchaeota from the same enzyme in members of the TACK and Asgard super-phyla, which showed considerable similarity to its eukaryal homologue Stt3. The results thus support the evolutionary proximity of Eukarya and the TACK and Asgard archaea.
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9
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Kelly JF, Vinogradov E, Stupak J, Robotham AC, Logan SM, Berezuk A, Khursigara CM, Jarrell KF. Identification of a novel N-linked glycan on the archaellins and S-layer protein of the thermophilic methanogen, Methanothermococcus thermolithotrophicus. J Biol Chem 2020; 295:14618-14629. [PMID: 32817340 DOI: 10.1074/jbc.ra120.012790] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/28/2020] [Indexed: 01/25/2023] Open
Abstract
Motility in archaea is facilitated by a unique structure termed the archaellum. N-Glycosylation of the major structural proteins (archaellins) is important for their subsequent incorporation into the archaellum filament. The identity of some of these N-glycans has been determined, but archaea exhibit extensive variation in their glycans, meaning that further investigations can shed light not only on the specific details of archaellin structure and function, but also on archaeal glycobiology in general. Here we describe the structural characterization of the N-linked glycan modifications on the archaellins and S-layer protein of Methanothermococcus thermolithotrophicus, a methanogen that grows optimally at 65 °C. SDS-PAGE and MS analysis revealed that the sheared archaella are composed principally of two of the four predicted archaellins, FlaB1 and FlaB3, which are modified with a branched, heptameric glycan at all N-linked sequons except for the site closest to the N termini of both proteins. NMR analysis of the purified glycan determined the structure to be α-d-glycero-d-manno-Hep3OMe6OMe-(1-3)-[α-GalNAcA3OMe-(1-2)-]-β-Man-(1-4)-[β-GalA3OMe4OAc6CMe-(1-4)-α-GalA-(1-2)-]-α-GalAN-(1-3)-β-GalNAc-Asn. A detailed investigation by hydrophilic interaction liquid ion chromatography-MS discovered the presence of several, less abundant glycan variants, related to but distinct from the main heptameric glycan. In addition, we confirmed that the S-layer protein is modified with the same heptameric glycan, suggesting a common N-glycosylation pathway. The M. thermolithotrophicus archaellin N-linked glycan is larger and more complex than those previously identified on the archaellins of related mesophilic methanogens, Methanococcus voltae and Methanococcus maripaludis This could indicate that the nature of the glycan modification may have a role to play in maintaining stability at elevated temperatures.
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Affiliation(s)
- John F Kelly
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada.
| | - Evgeny Vinogradov
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Jacek Stupak
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Anna C Robotham
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Susan M Logan
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Alison Berezuk
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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10
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Lu H, Pei C, Zhou H, Lü Y, He Y, Li Y, Han J, Xiang H, Eichler J, Jin C. Agl22 and Agl23 are involved in the synthesis and utilization of the lipid‐linked intermediates in the glycosylation pathways of the halophilic archaeaonHaloarcula hispanica. Mol Microbiol 2020; 114:762-774. [DOI: 10.1111/mmi.14577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Hua Lu
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Caixia Pei
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Hui Zhou
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Yang Lü
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Yun He
- Laboratory of Cellular and Molecular Tumor Immunology Institutes of Biology and Medical Sciences Jiangsu Laboratory of Infection Immunity Soochow University Suzhou China
| | - Yunsen Li
- Laboratory of Cellular and Molecular Tumor Immunology Institutes of Biology and Medical Sciences Jiangsu Laboratory of Infection Immunity Soochow University Suzhou China
| | - Jing Han
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Jerry Eichler
- Department of Life Sciences Ben Gurion University of the Negev Beersheva Israel
| | - Cheng Jin
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
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11
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Kightlinger W, Warfel KF, DeLisa MP, Jewett MC. Synthetic Glycobiology: Parts, Systems, and Applications. ACS Synth Biol 2020; 9:1534-1562. [PMID: 32526139 PMCID: PMC7372563 DOI: 10.1021/acssynbio.0c00210] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/11/2022]
Abstract
Protein glycosylation, the attachment of sugars to amino acid side chains, can endow proteins with a wide variety of properties of great interest to the engineering biology community. However, natural glycosylation systems are limited in the diversity of glycoproteins they can synthesize, the scale at which they can be harnessed for biotechnology, and the homogeneity of glycoprotein structures they can produce. Here we provide an overview of the emerging field of synthetic glycobiology, the application of synthetic biology tools and design principles to better understand and engineer glycosylation. Specifically, we focus on how the biosynthetic and analytical tools of synthetic biology have been used to redesign glycosylation systems to obtain defined glycosylation structures on proteins for diverse applications in medicine, materials, and diagnostics. We review the key biological parts available to synthetic biologists interested in engineering glycoproteins to solve compelling problems in glycoscience, describe recent efforts to construct synthetic glycoprotein synthesis systems, and outline exemplary applications as well as new opportunities in this emerging space.
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Affiliation(s)
- Weston Kightlinger
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Katherine F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Matthew P. DeLisa
- Department
of Microbiology, Cornell University, 123 Wing Drive, Ithaca, New York 14853, United States
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Weill Hall, Ithaca, New York 14853, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
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12
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Zaretsky M, Darnell CL, Schmid AK, Eichler J. N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility. Front Microbiol 2019; 10:1367. [PMID: 31275283 PMCID: PMC6591318 DOI: 10.3389/fmicb.2019.01367] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022] Open
Abstract
Halobacterium salinarum are halophilic archaea that display directional swimming in response to various environmental signals, including light, chemicals and oxygen. In Hbt. salinarum, the building blocks (archaellins) of the archaeal swimming apparatus (the archaellum) are N-glycosylated. However, the physiological importance of archaellin N-glycosylation remains unclear. Here, a tetrasaccharide comprising a hexose and three hexuronic acids decorating the five archaellins was characterized by mass spectrometry. Such analysis failed to detect sulfation of the hexuronic acids, in contrast to earlier reports. To better understand the physiological significance of Hbt. salinarum archaellin N-glycosylation, a strain deleted of aglB, encoding the archaeal oligosaccharyltransferase, was generated. In this ΔaglB strain, archaella were not detected and only low levels of archaellins were released into the medium, in contrast to what occurs with the parent strain. Mass spectrometry analysis of the archaellins in ΔaglB cultures did not detect N-glycosylation. ΔaglB cells also showed a slight growth defect and were impaired for motility. Quantitative real-time PCR analysis revealed dramatically reduced transcript levels of archaellin-encoding genes in the mutant strain, suggesting that N-glycosylation is important for archaellin transcription, with downstream effects on archaellum assembly and function. Control of AglB-dependent post-translational modification of archaellins could thus reflect a previously unrecognized route for regulating Hbt. salinarum motility.
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Affiliation(s)
- Marianna Zaretsky
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheba, Israel
| | | | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC, United States.,Center for Genomics and Computational Biology, Duke University, Durham, NC, United States
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheba, Israel
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13
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Zaretsky M, Roine E, Eichler J. Sialic Acid-Like Sugars in Archaea: Legionaminic Acid Biosynthesis in the Halophile Halorubrum sp. PV6. Front Microbiol 2018; 9:2133. [PMID: 30245679 PMCID: PMC6137143 DOI: 10.3389/fmicb.2018.02133] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/20/2018] [Indexed: 11/25/2022] Open
Abstract
N-glycosylation is a post-translational modification that occurs in all three domains. In Archaea, however, N-linked glycans present a degree of compositional diversity not observed in either Eukarya or Bacteria. As such, it is surprising that nonulosonic acids (NulOs), nine-carbon sugars that include sialic acids, pseudaminic acids, and legionaminic acids, are routinely detected as components of protein-linked glycans in Eukarya and Bacteria but not in Archaea. In the following, we report that the N-linked glycan attached to the S-layer glycoprotein of the haloarchaea Halorubrum sp. PV6 includes an N-formylated legionaminic acid. Analysis of the Halorubrum sp. PV6 genome led to the identification of sequences predicted to comprise the legionaminic acid biosynthesis pathway. The transcription of pathway genes was confirmed, as was the co-transcription of several of these genes. In addition, the activities of LegI, which catalyzes the condensation of 2,4-di-N-acetyl-6-deoxymannose and phosphoenolpyruvate to generate legionaminic acid, and LegF, which catalyzes the addition of cytidine monophosphate (CMP) to legionaminic acid, both heterologously expressed in Haloferax volcanii, were demonstrated. Further genome analysis predicts that the genes encoding enzymes of the legionaminic acid biosynthetic pathway are clustered together with sequences seemingly encoding components of the N-glycosylation pathway in this organism. In defining the first example of a legionaminic acid biosynthesis pathway in Archaea, the findings reported here expand our insight into archaeal N-glycosylation, an almost universal post-translational modification in this domain of life.
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Affiliation(s)
- Marianna Zaretsky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Elina Roine
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
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14
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Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U. Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax. Genes (Basel) 2018; 9:genes9030172. [PMID: 29558455 PMCID: PMC5867893 DOI: 10.3390/genes9030172] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/01/2018] [Accepted: 03/09/2018] [Indexed: 11/16/2022] Open
Abstract
Within the Haloferax genus, both the surface (S)-layer protein, and the glycans that can decorate it, vary between species, which can potentially result in many different surface types, analogous to bacterial serotypes. This variation may mediate phenotypes, such as sensitivity to different viruses and mating preferences. Here, we describe S-layer glycoproteins found in multiple Haloferax strains and perform comparative genomics analyses of major and alternative glycosylation clusters of isolates from two coastal sites. We analyze the phylogeny of individual glycosylation genes and demonstrate that while the major glycosylation cluster tends to be conserved among closely related strains, the alternative cluster is highly variable. Thus, geographically- and genetically-related strains may exhibit diverse surface structures to such an extent that no two isolates present an identical surface profile.
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Affiliation(s)
- Yarden Shalev
- School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Shannon M Soucy
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - J Peter Gogarten
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 8410501, Israel.
| | - Uri Gophna
- School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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15
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Elharar Y, Podilapu AR, Guan Z, Kulkarni SS, Eichler J. Assembling Glycan-Charged Dolichol Phosphates: Chemoenzymatic Synthesis of a Haloferax volcanii N-Glycosylation Pathway Intermediate. Bioconjug Chem 2017; 28:2461-2470. [PMID: 28809486 DOI: 10.1021/acs.bioconjchem.7b00436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-glycosylation, the covalent attachment of glycans to select protein target Asn residues, is a post-translational modification performed by all three domains of life. In the halophilic archaea Haloferax volcanii, in which understanding of this universal protein-processing event is relatively well-advanced, genes encoding the components of the archaeal glycosylation (Agl) pathway responsible for the assembly and attachment of an N-linked pentasaccharide have been identified. As elsewhere, the N-linked glycan is assembled on phosphodolichol carriers before transfer to target Asn residues. However, as little is presently known of the Hfx. volcanii Agl pathway at the protein level, the seemingly unique ability of Archaea to use dolichol phosphate (DolP) as the glycan lipid carrier, rather than dolichol pyrophosphate used by eukaryotes, remains poorly understood. With this in mind, a chemoenzymatic approach was taken to biochemically study AglG, one of the five glycosyltransferases of the pathway. Accordingly, a novel regio- and stereoselective reduction of naturally isolated polyprenol gave facile access to S-dolichol via asymmetric transfer hydrogenation under very mild conditions. This compound was used to generate glucose-charged DolP, a precursor of the N-linked pentasaccharide, as well as DolP-glucose-glucuronic acid and DolP-glucuronic acid. AglG, purified from Hfx. volcanii membranes in hypersaline conditions, like those encountered in situ, was subsequently combined with uridine diphosphate (UDP)-glucuronic acid and DolP-glucose to yield DolP-glucose-glucuronic acid. The in vitro system for the study of AglG activity developed here represents the first such tool for studying halophilic glycosyltransferases and will allow for a detailed understanding of archaeal N-glycosylation.
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Affiliation(s)
- Yifat Elharar
- Department of Life Sciences, Ben Gurion University of the Negev , Beersheva 8410501, Israel
| | - Ananda Rao Podilapu
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Suvarn S Kulkarni
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev , Beersheva 8410501, Israel
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16
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Shalev Y, Turgeman-Grott I, Tamir A, Eichler J, Gophna U. Cell Surface Glycosylation Is Required for Efficient Mating of Haloferax volcanii. Front Microbiol 2017; 8:1253. [PMID: 28725221 PMCID: PMC5496957 DOI: 10.3389/fmicb.2017.01253] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/21/2017] [Indexed: 01/30/2023] Open
Abstract
Halophilic archaea use a fusion-based mating system for lateral gene transfer across cells, yet the molecular mechanisms involved remain unknown. Previous work implied that cell fusion involves cell-cell recognition since fusion occurs more efficiently between cells from the same species. Long believed to be restricted only to Eukarya, it is now known that cells of all three domains of life perform N-glycosylation, the covalent attachment of glycans to select target asparagine residues in proteins, and that this post-translational modification is common for archaeal cell surface proteins. Here, we show that differences in glycosylation of the Haloferax volcanii surface-layer glycoprotein, brought about either by changing medium salinity or by knocking out key glycosylation genes, reduced mating success. Thus, different glycosylation patterns are likely to underlie mating preference in halophilic archaea, contributing to speciation processes.
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Affiliation(s)
- Yarden Shalev
- School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Israela Turgeman-Grott
- School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Adi Tamir
- Department of Life Sciences, Ben-Gurion University of the NegevBeersheva, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the NegevBeersheva, Israel
| | - Uri Gophna
- School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel Aviv, Israel
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17
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Eichler J, Guan Z. Lipid sugar carriers at the extremes: The phosphodolichols Archaea use in N-glycosylation. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:589-599. [PMID: 28330764 DOI: 10.1016/j.bbalip.2017.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 11/28/2022]
Abstract
N-glycosylation, a post-translational modification whereby glycans are covalently linked to select Asn residues of target proteins, occurs in all three domains of life. Across evolution, the N-linked glycans are initially assembled on phosphorylated cytoplasmically-oriented polyisoprenoids, with polyprenol (mainly C55 undecaprenol) fulfilling this role in Bacteria and dolichol assuming this function in Eukarya and Archaea. The eukaryal and archaeal versions of dolichol can, however, be distinguished on the basis of their length, degree of saturation and by other traits. As is true for many facets of their biology, Archaea, best known in their capacity as extremophiles, present unique approaches for synthesizing phosphodolichols. At the same time, general insight into the assembly and processing of glycan-bearing phosphodolichols has come from studies of the archaeal enzymes responsible. In this review, these and other aspects of archaeal phosphodolichol biology are addressed.
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Affiliation(s)
- Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 84105, Israel.
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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18
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Complementation of an aglB Mutant of Methanococcus maripaludis with Heterologous Oligosaccharyltransferases. PLoS One 2016; 11:e0167611. [PMID: 27907170 PMCID: PMC5131992 DOI: 10.1371/journal.pone.0167611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 11/17/2016] [Indexed: 01/04/2023] Open
Abstract
The oligosaccharyltransferase is the signature enzyme for N-linked glycosylation in all domains of life. In Archaea, this enzyme termed AglB, is responsible for transferring lipid carrier-linked glycans to select asparagine residues in a variety of target proteins including archaellins, S-layer proteins and pilins. This study investigated the ability of a variety of AglBs to compensate for the oligosaccharyltransferase activity in Methanococcus maripaludis deleted for aglB, using archaellin FlaB2 as the reporter protein since all archaellins in Mc. maripaludis are modified at multiple sites by an N-linked tetrasaccharide and this modification is required for archaellation. In the Mc. maripaludis ΔaglB strain FlaB2 runs as at a smaller apparent molecular weight in western blots and is nonarchaellated. We demonstrate that AglBs from Methanococcus voltae and Methanothermococcus thermolithotrophicus functionally replaced the oligosaccharyltransferase activity missing in the Mc. maripaludis ΔaglB strain, both returning the apparent molecular weight of FlaB2 to wildtype size and restoring archaellation. This demonstrates that AglB from Mc. voltae has a relaxed specificity for the linking sugar of the transferred glycan since while the N-linked glycan present in Mc. voltae is similar to that of Mc. maripaludis, the Mc. voltae glycan uses N-acetylglucosamine as the linking sugar. In Mc. maripaludis that role is held by N-acetylgalactosamine. This study also identifies aglB from Mtc. thermolithotrophicus for the first time by its activity. Attempts to use AglB from Methanocaldococcus jannaschii, Haloferax volcanii or Sulfolobus acidocaldarius to functionally replace the oligosaccharyltransferase activity missing in the Mc. maripaludis ΔaglB strain were unsuccessful.
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19
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Guan Z, Delago A, Nußbaum P, Meyer B, Albers SV, Eichler J. N-glycosylation in the thermoacidophilic archaeon Sulfolobus acidocaldarius involves a short dolichol pyrophosphate carrier. FEBS Lett 2016; 590:3168-78. [PMID: 27490243 DOI: 10.1002/1873-3468.12341] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 01/31/2023]
Abstract
N-glycosylation is a post-translational modification that occurs across evolution. In the thermoacidophilic archaea Sulfolobus acidocaldarius, glycoproteins are modified by an N-linked tribranched hexasaccharide reminiscent of the N-glycans assembled in Eukarya. Previously, hexose-bearing dolichol phosphate was detected in a S. acidocaldarius Bligh-Dyer lipid extract. Here, we used a specialized protocol for extracting lipid-linked oligosaccharides to detect a dolichol pyrophosphate bearing the intact hexasaccharide, as well as its biosynthetic intermediates. Furthermore, evidence for N-glycosylation of two S. acidocaldarius proteins by the same hexasaccharide and its derivatives was collected. These findings thus provide novel insight into archaeal N-glycosylation.
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Affiliation(s)
- Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Antonia Delago
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Phillip Nußbaum
- Molecular Biology of Archaea, Institute for Biology II-Microbiology, Albert-Ludwigs-University of Freiburg, Germany
| | - Benjamin Meyer
- Molecular Biology of Archaea, Institute for Biology II-Microbiology, Albert-Ludwigs-University of Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute for Biology II-Microbiology, Albert-Ludwigs-University of Freiburg, Germany
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel.
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20
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N-linked glycosylation of N48 is required for equilibrative nucleoside transporter 1 (ENT1) function. Biosci Rep 2016; 36:BSR20160063. [PMID: 27480168 PMCID: PMC5006311 DOI: 10.1042/bsr20160063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/01/2016] [Indexed: 11/29/2022] Open
Abstract
Our study confirmed that Asn48 of hENT1 is the only N-glycosylated residue when expressed in HEK293 cells, and loss of the N-glycan resulted in less hENT1 at the plasma membrane, as well as a loss of function and protein–protein self-interaction. Human equilibrative nucleoside transporter 1 (hENT1) transports nucleosides and nucleoside analogue drugs across cellular membranes and is necessary for the uptake of many anti-cancer, anti-parasitic and anti-viral drugs. Previous work, and in silico prediction, suggest that hENT1 is glycosylated at Asn48 in the first extracellular loop of the protein and that glycosylation plays a role in correct localization and function of hENT1. Site-directed mutagenesis of wild-type (wt) hENT1 removed potential glycosylation sites. Constructs (wt 3xFLAG-hENT1, N48Q-3xFLAG-hENT1 or N288Q-3xFLAG-hENT2) were transiently transfected into HEK293 cells and cell lysates were treated with or without peptide–N-glycosidase F (PNGase-F), followed by immunoblotting analysis. Substitution of N48 prevents hENT1 glycosylation, confirming a single N-linked glycosylation site. N48Q-hENT1 protein is found at the plasma membrane in HEK293 cells but at lower levels compared with wt hENT1 based on S-(4-nitrobenzyl)-6-thioinosine (NBTI) binding analysis (wt 3xFLAG-ENT1 Bmax, 41.5±2.9 pmol/mg protein; N48Q-3xFLAG-ENT1 Bmax, 13.5±0.45 pmol/mg protein) and immunofluorescence microscopy. Although present at the membrane, chloroadenosine transport assays suggest that N48Q-hENT1 is non-functional (wt 3xFLAG-ENT1, 170.80±44.01 pmol/mg protein; N48Q-3xFLAG-ENT1, 57.91±17.06 pmol/mg protein; mock-transfected 74.31±19.65 pmol/mg protein). Co-immunoprecipitation analyses suggest that N48Q ENT1 is unable to interact with self or with wt hENT1. Based on these data we propose that glycosylation at N48 is critical for the localization, function and oligomerization of hENT1.
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21
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Schäffer C, Messner P. Emerging facets of prokaryotic glycosylation. FEMS Microbiol Rev 2016; 41:49-91. [PMID: 27566466 DOI: 10.1093/femsre/fuw036] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/17/2016] [Accepted: 08/01/2016] [Indexed: 12/16/2022] Open
Abstract
Glycosylation of proteins is one of the most prevalent post-translational modifications occurring in nature, with a wide repertoire of biological implications. Pathways for the main types of this modification, the N- and O-glycosylation, can be found in all three domains of life-the Eukarya, Bacteria and Archaea-thereby following common principles, which are valid also for lipopolysaccharides, lipooligosaccharides and glycopolymers. Thus, studies on any glycoconjugate can unravel novel facets of the still incompletely understood fundamentals of protein N- and O-glycosylation. While it is estimated that more than two-thirds of all eukaryotic proteins would be glycosylated, no such estimate is available for prokaryotic glycoproteins, whose understanding is lagging behind, mainly due to the enormous variability of their glycan structures and variations in the underlying glycosylation processes. Combining glycan structural information with bioinformatic, genetic, biochemical and enzymatic data has opened up an avenue for in-depth analyses of glycosylation processes as a basis for glycoengineering endeavours. Here, the common themes of glycosylation are conceptualised for the major classes of prokaryotic (i.e. bacterial and archaeal) glycoconjugates, with a special focus on glycosylated cell-surface proteins. We describe the current knowledge of biosynthesis and importance of these glycoconjugates in selected pathogenic and beneficial microbes.
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Affiliation(s)
- Christina Schäffer
- Department of NanoBiotechnology, Institute of Biologically Inspired Materials, NanoGlycobiology unit, Universität für Bodenkultur Wien, A-1180 Vienna, Austria
| | - Paul Messner
- Department of NanoBiotechnology, Institute of Biologically Inspired Materials, NanoGlycobiology unit, Universität für Bodenkultur Wien, A-1180 Vienna, Austria
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22
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Taguchi Y, Fujinami D, Kohda D. Comparative Analysis of Archaeal Lipid-linked Oligosaccharides That Serve as Oligosaccharide Donors for Asn Glycosylation. J Biol Chem 2016; 291:11042-54. [PMID: 27015803 DOI: 10.1074/jbc.m115.713156] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Indexed: 11/06/2022] Open
Abstract
The glycosylation of asparagine residues is the predominant protein modification in all three domains of life. An oligosaccharide chain is preassembled on a lipid-phospho carrier and transferred onto asparagine residues by the action of a membrane-bound enzyme, oligosaccharyltransferase. The oligosaccharide donor for the oligosaccharyl transfer reaction is dolichol-diphosphate-oligosaccharide in Eukaryota and polyprenol-diphosphate-oligosaccharide in Eubacteria. The donor in some archaeal species was reportedly dolichol-monophosphate-oligosaccharide. Thus, the difference in the number of phosphate groups aroused interest in whether the use of the dolichol-monophosphate type donors is widespread in the domain Archaea. Currently, all of the archaeal species with identified oligosaccharide donors have belonged to the phylum Euryarchaeota. Here, we analyzed the donor structures of two species belonging to the phylum Crenarchaeota, Pyrobaculum calidifontis and Sulfolobus solfataricus, in addition to two species from the Euryarchaeota, Pyrococcus furiosus and Archaeoglobus fulgidus The electrospray ionization tandem mass spectrometry analyses confirmed that the two euryarchaeal oligosaccharide donors were the dolichol-monophosphate type and newly revealed that the two crenarchaeal oligosaccharide donors were the dolichol-diphosphate type. This novel finding is consistent with the hypothesis that the ancestor of Eukaryota is rooted within the TACK (Thaum-, Aig-, Cren-, and Korarchaeota) superphylum, which includes Crenarchaea. Our comprehensive study also revealed that one archaeal species could contain two distinct oligosaccharide donors for the oligosaccharyl transfer reaction. The A. fulgidus cells contained two oligosaccharide donors bearing oligosaccharide moieties with different backbone structures, and the S. solfataricus cells contained two oligosaccharide donors bearing stereochemically different dolichol chains.
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Affiliation(s)
| | | | - Daisuke Kohda
- From the Division of Structural Biology and Research Centers for Advanced Immunology and Live-Protein Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
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23
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Yao J, Guo H, Chaiprasongsuk M, Zhao N, Chen F, Yang X, Guo H. Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes. Biochemistry 2015; 54:5366-75. [PMID: 26244568 DOI: 10.1021/acs.biochem.5b00638] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although one of an enzyme's hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. It is known that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. Here we report the results of quantum mechanical/molecular mechanical simulations and an experimental study of salicylic acid binding protein 2 (SABP2). SABP2 has promiscuous esterase activity toward a series of substrates but shows a high activity toward its natural substrate, methyl salicylate (MeSA). Our results demonstrate that this enzyme may use substrate-assisted catalysis involving the hydroxyl group from MeSA to enhance the activity and achieve substrate discrimination.
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Affiliation(s)
- Jianzhuang Yao
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Minta Chaiprasongsuk
- Department of Plant Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Nan Zhao
- Department of Plant Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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24
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Chang MM, Imperiali B, Eichler J, Guan Z. N-Linked Glycans Are Assembled on Highly Reduced Dolichol Phosphate Carriers in the Hyperthermophilic Archaea Pyrococcus furiosus. PLoS One 2015; 10:e0130482. [PMID: 26098850 PMCID: PMC4476749 DOI: 10.1371/journal.pone.0130482] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 05/19/2015] [Indexed: 12/26/2022] Open
Abstract
In all three domains of life, N-glycosylation begins with the assembly of glycans on phosphorylated polyisoprenoid carriers. Like eukaryotes, archaea also utilize phosphorylated dolichol for this role, yet whereas the assembled oligosaccharide is transferred to target proteins from dolichol pyrophosphate in eukaryotes, archaeal N-linked glycans characterized to date are derived from a dolichol monophosphate carrier, apart from a single example. In this study, glycan-charged dolichol phosphate from the hyperthermophile Pyrococcus furiosus was identified and structurally characterized. Normal and reverse phase liquid chromatography-electrospray ionization mass spectrometry revealed the existence of dolichol phosphate charged with the heptasaccharide recently described in in vitro studies of N-glycosylation on this species. As with other described archaeal dolichol phosphates, the α- and ω-terminal isoprene subunits of the P. furiosus lipid are saturated, in contrast to eukaryal phosphodolichols that present only a saturated α-position isoprene subunit. Interestingly, an additional 1-4 of the 12-14 isoprene subunits comprising P. furiosus dolichol phosphate are saturated, making this lipid not only the longest archaeal dolichol phosphate described to date but also the most highly saturated.
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Affiliation(s)
- Michelle M. Chang
- Departments of Biology and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Barbara Imperiali
- Departments of Biology and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University, Beersheva 84105, Israel
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States of America
- * E-mail:
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Kandiba L, Eichler J. Deciphering a pathway of Halobacterium salinarum N-glycosylation. Microbiologyopen 2014; 4:28-40. [PMID: 25461760 PMCID: PMC4335974 DOI: 10.1002/mbo3.215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 08/15/2014] [Accepted: 08/20/2014] [Indexed: 12/14/2022] Open
Abstract
Genomic analysis points to N-glycosylation as being a common posttranslational modification in Archaea. To date, however, pathways of archaeal N-glycosylation have only been described for few species. With this in mind, the similarities of N-linked glycans decorating glycoproteins in the haloarchaea Haloferax volcanii and Halobacterium salinarum directed a series of bioinformatics, genetic, and biochemical experiments designed to describe that Hbt. salinarum pathway responsible for biogenesis of one of the two N-linked oligosaccharides described in this species. As in Hfx. volcanii, where agl (archaeal glycosylation) genes that encode proteins responsible for the assembly and attachment of a pentasaccharide to target protein Asn residues are clustered in the genome, Hbt. salinarum also contains a group of clustered homologous genes (VNG1048G-VNG1068G). Introduction of these Hbt. salinarum genes into Hfx. volcanii mutant strains deleted of the homologous sequence restored the lost activity. Moreover, transcription of the Hbt. salinarum genes in the native host, as well as in vitro biochemical confirmation of the predicted functions of several of the products of these genes provided further support for assignments made following bioinformatics and genetic experiments. Based on the results obtained in this study, the first description of an N-glycosylation pathway in Hbt. salinarum is offered.
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Affiliation(s)
- Lina Kandiba
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
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Eichler J, Arbiv A, Cohen-Rosenzweig C, Kaminski L, Kandiba L, Konrad Z. N-glycosylation in Haloferax volcanii: adjusting the sweetness. Front Microbiol 2013; 4:403. [PMID: 24399998 PMCID: PMC3871713 DOI: 10.3389/fmicb.2013.00403] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 12/06/2013] [Indexed: 12/23/2022] Open
Abstract
Long believed to be restricted to Eukarya, it is now known that cells of all three domains of life perform N-glycosylation, the covalent attachment of glycans to select target protein asparagine residues. Still, it is only in the last decade that pathways of N-glycosylation in Archaea have been delineated. In the haloarchaeon Haloferax volcanii, a series of Agl (archaeal glycosylation) proteins is responsible for the addition of an N-linked pentasaccharide to modified proteins, including the surface (S)-layer glycoprotein, the sole component of the surface layer surrounding the cell. The S-layer glycoprotein N-linked glycosylation profile changes, however, as a function of surrounding salinity. Upon growth at different salt concentrations, the S-layer glycoprotein is either decorated by the N-linked pentasaccharide introduced above or by both this pentasaccharide as well as a tetrasaccharide of distinct composition. Recent efforts have identified Agl5–Agl15 as components of a second Hfx. volcanii N-glycosylation pathway responsible for generating the tetrasaccharide attached to S-layer glycoprotein when growth occurs in 1.75 M but not 3.4 M NaCl-containing medium.
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Affiliation(s)
- Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev Beersheva, Israel
| | - Adi Arbiv
- Department of Life Sciences, Ben Gurion University of the Negev Beersheva, Israel
| | | | - Lina Kaminski
- Department of Life Sciences, Ben Gurion University of the Negev Beersheva, Israel
| | - Lina Kandiba
- Department of Life Sciences, Ben Gurion University of the Negev Beersheva, Israel
| | - Zvia Konrad
- Department of Life Sciences, Ben Gurion University of the Negev Beersheva, Israel
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